On 17:05 Tue 20 Jan , Paul Emsley wrote: > Roger Rowlett wrote: >> I will second noting the loss of arp_waters in CCP4 6.1. I know there >> is a "find waters" option in Coot 0.5.2 under "Calculate...Other >> modeling tools", and perhaps this is adequate, but it doesn't seem to >> have as many options for fine-tuning as arp_waters did. Coot allows >> for finding waters above a certain sigma value; arp_waters allowed >> this option plus setting minimum and maximum hydrogen bonding >> distances between heavy atoms. > > May I be so bold as to point you to the documentation? > > http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_5.html#SEC127 > > If you want to use a command line program, type findwaters on the > command line and it will give a short description of the parameters it > takes. > (It is also documented in section 9.1 of the manual.)
One of the major reasons our lab started using Coot instead of O is that you didn't have to memorize or look up a million obscure functions to do everything. It was in the Coot GUI. When we're training new people, this helps immensely for the 99% of them who have never used Linux or any type of command line before. If there isn't a GUI for it, it effectively doesn't exist for them. I would enjoy understanding what the philosophy of the Coot developers is on this matter. -- Thanks, Donnie Donnie Berkholz Developer, Gentoo Linux Blog: http://dberkholz.wordpress.com
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